I dont understand your question. If you migrate the WebSphere app from WAS5.1 to WAS7, you should continue to have the same artifacts that you used in WAS5.1. So, if you are migrating a Web App, you should have, or should produce with the same procedures, the .war file from your repository.
To simplify Application Migration, check out the IBM Migration Toolkit - a free tool that can help you with the migration. The link is:
www.ibm.com/developerworks/websphere/dow...
So, I am not sure what .war file you are looking for.